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General description of the gene and encoded protein(s) using information from HGNC and Ensembl, as well as predictions made as well as predictions made by the Human Protein Atlas project.
All transcripts of all genes have been analyzed regarding the location(s) of corresponding protein based on prediction methods for signal peptides and transmembrane regions.
Genes with at least one transcript predicted to encode a secreted protein, according to prediction methods or to UniProt location data, have been further annotated and classified with the aim to determine if the corresponding protein(s) are secreted or actually retained in intracellular locations or membrane-attached.
Remaining genes, with no transcript predicted to encode a secreted protein, will be assigned the prediction-based location(s).
The annotated location overrules the predicted location, so that a gene encoding a predicted secreted protein that has been annotated as intracellular will have intracellular as the final location.
All genes with at least one predicted secreted isoform have been annotated and classified with the aim to determine if the corresponding protein(s) are:
secreted into blood
locally secreted
or actually being attached to membrane or retained in intracellular locations like mitochondria, endoplasmatic reticulum (ER), Golgi apparatus or lysosomes.
The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: lineage enriched, group enriched, lineage enhanced, low lineage specificity and not detected. Lineages include B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells.
The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected. Lineages include B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells.
The RNA specificity category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: cell type enriched, group enriched, cell type enhanced, low cell type specificity and not detected.
The RNA distribution category is based on mRNA expression levels in the analyzed samples based on data from HPA. The categories include: detected in all, detected in many, detected in some, detected in single and not detected.
The blood-based immunoassay category applies to actively secreted proteins and is based on plasma or serum protein concentrations established with enzyme-linked immunosorbent assays, compiled from a literature search. The categories include: detected and not detected, where detection refers to a concentration found in the literature search.
Detection or not of the gene in blood, based on spectral count estimations from a publicly available mass spectrometry-based plasma proteomics data set obtained from the PeptideAtlas.
Not detected
BLOOD CELL TYPE EXPRESSION (RNA)i
Blood cell type expression overview shows RNA-seq data from three different sources: Internally generated Human Protein Atlas (HPA) data, as well as data generated by (Monaco et al) and (Schmiedel et al). Color-coding is based on blood cell type lineages, including B-cells, T-cells, NK-cells, monocytes, granulocytes and dendritic cells as well as total PBMC. To access sample data, click on tissue name or bar.
Consensus dataseti
The resulting transcript expression values, denoted Normalized eXpression (NX), resulting from the internal normalization pipeline for 18 blood cell types and total peripheral blood mononuclear cells (PBMC).
RNA cell type specificity: Group enriched (memory CD4 T-cell, T-reg)
HPA scaled dataseti
pTPM values are calculated by scaling all TPM values per sample to a sum of 1 million TPM to compensate for the previously removed non-coding transcripts and are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC).
pTPM values are calculated by scaling all TPM values per sample to a sum of 1 million TPM to compensate for the previously removed non-coding transcripts and are visualized for 29 blood cell types and total peripheral blood mononuclear cells (PBMC) from Monaco et al.
Plasma or serum concentrations of the genes annotated as actively secreted to blood. Up to three values for each gene were compiled from a literature search limited to studies where the protein concentration was determined using an antibody-based assay such as enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA) or immunoturbidimetry (IT).
PROTEIN CONCENTRATION IN PLASMA - MASS SPECTROMETRYi
The protein concentration in blood is quantified by mass spectrometry-based plasma proteomics and estimated from spectral counts in a publicly available data set obtained from the PeptideAtlas.
Protein target not detected in plasma for reference set (Peptide atlas) by mass spectrometry
PROTEIN DETECTED IN PLASMA - PROXIMITY EXTENSION ASSAYi
The protein profiling results based on proximity extension assays (Olink) for a longitudinal wellness study covering 86 individuals with four visits during one year at three months intervals. Protein expression levels are reported as Normalized Protein Expression (NPX).
The Human Protein Atlas project is funded
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